Background: Modern endovascular thrombectomy (MET), using stent retrievers or large-bore distal aspiration catheters in stroke patients with acute basilar artery occlusion (BAO), is routinely performed to date. However, more than 35% of BAO patients treated with MET die within 90 days despite high recanalization rates. The purpose of this study is to investigate the parameters associated with 90-day mortality in patients with BAO after MET. Methods: We analyzed 117 consecutive BAO patients included in the Endovascular Treatment in Ischemic Stroke prospective clinical registry of consecutive acute ischemic stroke patients treated with MET (60 patients [51.3%] treated with a stent retriever as first-line technique) between March 2010 and April 2017. Successful recanalization was defined as modified thrombolysis In cerebral infarction scores 2b-3 at the end of MET, and mortality was defined as modified Rankin Scale 6 at 90 days. Associations of baseline characteristics (patient and treatment characteristics) and intermediate outcomes (recanalization, complications) with 90-day mortality were investigated in univariate and multivariate analyses. Results: Overall successful recanalization rate was 79.5, and 41.9% (95% CI 32.8–51.0%) of patients died within 90 days after MET. Patients with successful recanalization had a lower mortality rate (32.9 vs. 74.4%; p < 0.001). Failure of successful recanalization was an independent predictor of mortality (OR 5.1; 95% CI 1.34–19.33). In multivariate analysis, age ≥60 years (OR 6.37; 95% CI 1.74–23.31), admission National Institute of Health Stroke Scale (NIHSS) ≥13 (OR 4.62; 95% CI 1.42–15.03), lower posterior circulation-Alberta Stroke Program Early CT Score (pc-ASPECTS; OR 1.71; 95% CI 1.19–2.44), use of antithrombotic medication prior to stroke onset (OR 3.38; 95% CI 1.03–11.08), absence of intravenous thrombolysis (OR 3.36; 95% CI 1.12–10.03), and angioplasty/stenting of the basilar artery (OR 4.71; 95% CI 1.34–16.54) were independent predictors for mortality after MET. Conclusions: Failure of successful recanalization was a strong predictor for mortality. In the setting of recanalization, age, admission NIHSS, pc-ASPECTS, absence of intravenous thrombolysis, and angioplasty/stenting of the basilar artery were also independent predictors for mortality after MET of BAO patients.